7UP8

Crystal structure of C-terminal Domain of MSK1 in complex with covalently bound pyrrolopyrimidine compound 27 (co-crystal)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289Plate 320267f8, puck cnl-6-9.Screen:Morpheus_D8_F8_G8_Index_E7. To prepare the ligand complex, PID7059-1 was exchanged to 25 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 1 mM BME (dillution buffer) using a GE (GE28-9180-04) spin column. The protein was diluted to 1 mg/ml in dilution bufffer and 150 ?M UCB1710266 in 100% DMSO_D6 was added. The complex was incubated at 4 C for an hour, then excess ligand was removed by dialysis using a D-tube dialyzer in 250 ml dilution buffer, overnight at 4 ?C. The following day the protein was concentrated to 10.1 mg/ml and setup 200:100 ul protein:well solution. Crystals were flash frozen in 100% well solution
Crystal Properties
Matthews coefficientSolvent content
2.3146.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.52α = 90
b = 90.91β = 90
c = 136.56γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002021-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.95099.60.1030.1190.99510.994.0021477850.492
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.981000.5590.6430.8242.74.103

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEin-house model2.948.21.3414772154499.620.19420.18630.2625057.99
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.9618
f_angle_d0.78
f_chiral_restr0.0464
f_plane_restr0.0057
f_bond_d0.0054
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4398
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms32

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing
Cootmodel building